Identification of Poly(ethylene glycol) and Poly(ethylene glycol)-Based Detergents Using Peptide Search Engines

Poly­(ethylene
glycol) (PEG) is one of the most common polymer contaminations
in mass spectrometry (MS) samples. At present, the detection of PEG
and other polymers relies largely on manual inspection of raw data,
which is laborious and frequently difficult due to sample complexity
and retention characteristics of polymer species in reversed-phase
chromatography. We developed a new strategy for the automated identification
of PEG molecules from tandem mass spectrometry (MS/MS) data using
protein identification algorithms in combination with a database containing “PEG–proteins”.
Through definition of variable modifications, we extend the approach
for the identification of commonly used PEG-based detergents. We exemplify
the identification of different types of polymers by static nanoelectrospray
tandem mass spectrometry (nanoESI-MS/MS) analysis of pure detergent
solutions and data analysis using Mascot. Analysis of liquid chromatography–tandem
mass spectrometry (LC–MS/MS) runs of a PEG-contaminated sample
by Mascot identified 806 PEG spectra originating from four PEG species
using a defined set of modifications covering PEG and common PEG-based
detergents. Further characterization of the sample for unidentified
PEG species using error-tolerant and mass-tolerant searches resulted
in identification of 3409 and 3187 PEG-related MS/MS spectra, respectively.
We further demonstrate the applicability of the strategy for Protein
Pilot and MaxQuant.